Identify and profile Phytophthora present in a nursery
Are either of these statements true? (not accounting for primer choice…)
NJ tree of ITS1 regions from cocoa-associated Phytophthora spp. Appiah et al. (2004) Plant Path. doi:10.1111/j.0032-0862.2004.00980.x
BLAST/HMMer) against sequenced genomesBLAST hits with ITS1 query
BUSCO)BUSCO gene coverage = estimated copy number
47 sequences from P. infestans T30-4
GRAbB, MITObim, and riboSEEDIf there is more than one ITS1 sequence per isolate…
SWARMFastQC to clean readsPEAR to assemble readsSWARM to cluster reads (unsupervised) for OTUsPCRMIX96 testing: 10 known species
PIPITS (requires database development)